Hi,
No, stopping core2 have no effect on mode transition.
I recommend you to first have a look on some of our reference examples:
MPC5 software example list
and read reference manual boot chapter carefully.
Your boot header is 0x005A0001. This means, only core2 is active after reset release.
You need to enable core0 in your SW (startup most probably). Some of default startups starts the other cores, like GHS delivered startup.
When your core0 is running. You can perform mode transition. There is only one ME module so whole micro is switched to target mode.
Make sure that you have stable target mode clock before transition. refer to clocking chapter and to mode entry chapter of reference manual.
As I said I was able to execute your code with debugger with no issues multiple times.
Peter